Novel xylanase from trichoderma reesei, method for production thereof, and methods employing this enzyme

ABSTRACT

The present invention is directed to novel xylanases (referred to as XYL-IV) and to nucleic acid molecules encoding those xylanases. Also provided herein are vectors and host cells including those nucleic acid sequences, antibodies which bind to the xylanases of the present invention, methods for producing the xylanases of the present invention, and methods employing the xylanases of the present invention.

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This Application claims priority to U.S. Ser. No. 60/173,889, filed Dec. 30, 1999.

GOVERNMENT SPONSORED RESEARCH AND DEVELOPMENT

[0002] Not Applicable.

BACKGROUND OF THE INVENTION

[0003] The complex structure of wood includes cellulose, hemicellulose and lignin, along with other minor components. Lignin is associated with cellulose and hemicellulose, and is probably partially covalently bound to both cellulose and hemicellulose. In the paper-making process, lignin is generally removed from the wood pulp since it lends a brownish color, reduces strength and imparts other undesirable characteristics to the finished product. Removal of lignin can be achieved in many ways.

[0004] A majority of the lignin is initially removed from wood pulp through chemical pulping (e.g., the Kraft process). In the subsequent bleaching process, chemical pulp is routinely reacted with chlorine and other delignifying chemicals to further remove lignin and then reacted with bleaching agents to modify the lignin from pulp, providing a stable brightened pulp. However, the treatment with chlorine is undesirable from an environmental standpoint because the resulting effluents contain a large number of toxic compounds (e.g., chlorinated phenolics). Concern about the environmental harmful effects caused by pulp bleaching with chlorine containing chemicals has driven the industry to seek alternative bleaching methods.

[0005] Attempts to use xylanases and other enzymes derived from fungal and bacterial sources to enhance delignification and brightening, while lowering or eliminating the use of chlorine chemicals, have been described in the literature. However, existing enzyme systems generally do not readily achieve degradation of hemicellulose or delignification to a sufficient extent. The extent of hemicellulose degradation and delignification could be improved by employing additional xylanases that cleave xylan in a different manner or that act synergistically with other xylanases, hemicellulases, other enzymes, or even chemicals.

[0006] Numerous xylanases from fungal and bacterial microorganisms have been identified and characterized. (See, e.g., U.S. Pat. No. 5,437,992; Coughlin, M. P. supra; Biely, P. et al., Proceedings of the second TRICEL symposium on Trichoderma reesei Cellulases and Other Hydrolases, Espoo 1993, P. Souminen and T. Reinikainen eds., Foundation for Biotechnical and Industrial Fermentation Research 8:125-135 (1993)). In particular, three specific xylanases (XYL-I, XYL-II, and XYL-III) have been identified in T. reesei (Tenkanen, et al., Enzyme Microb. Technol. 14:566 (1992); Törrönen, et al., Bio/Technology 10:1461 (1992); and Xu, et al., Appl. Microbiol. Biotechnol. 49:718 (1998)).

[0007] Although numerous xylanases have been described in the literature, the need still exists to identify novel xylanases that are more effective in applications relating to animal feed, grain processing, biofuels, cleaning, fabric care, chemicals, plant processing, and delignifying and brightening of pulp and paper.

SUMMARY OF THE INVENTION

[0008] Applicants have identified cDNA clones that encode a novel xylanase referred to herein as XYL-IV and have certain sequence identity to previously-described xylanases.

[0009] In one embodiment, the invention provides an isolated nucleic acid molecule including DNA encoding XYL-IV. In certain aspects, the isolated nucleic acid includes DNA encoding an XYL-IV having the amino acid sequence of FIG. 2 (SEQ ID NO:2), or is complementary to such encoding nucleic acid sequences. Preferably, the DNA encoding a XYL-IV protein is derived from a microorganism, preferably a fungus or a bacterium. Preferably, the DNA is derived from a filamentous fungus such as Trichoderma spp., Humicola spp., Neurospora spp., Aspergillus spp., Fusarium spp., Penicillium spp., or Gliocladium spp., more preferably from Trichoderma spp. Also preferably, the DNA includes the nucleotide sequence of SEQ ID NO:1. Alternately, the DNA has at least 50%, 60%, or 70%, preferably at least 85% or 90%, sequence identity with the nucleotide sequence of SEQ ID NO: 1, or includes a derivative of the nucleotide sequence of SEQ ID NO: 1, wherein the DNA encodes a XYL-IV protein which cleaves xylan, branched xylan or xylooligosaccharides. Vectors including such DNA, host cells having been transformed with such vectors and fermentation broths produced by such transformed host cells are also within the scope of the present invention.

[0010] Another embodiment of the present invention provides a partially or wholly isolated XYL-IV protein. Preferably, the XYL-IV is derived from a microorganism, preferably a fungus or a bacterium. Preferably, the XYL-UV is derived from a filamentous fungus, more preferably from a filamentous fungus such as Trichoderma spp., Humicola spp., Neurospora spp., Aspergillus spp., Fusarium spp., Penicillium spp., or Gliocladium spp., and most preferably from Trichoderma spp. In particular, the invention provides isolated native sequence XYL-IV, which in one embodiment, includes an amino acid sequence including residues 1 to 465 of FIG. 2 (SEQ ID NO:2). In a preferred embodiment of the present invention, the XYL-IV includes an amino acid sequence of SEQ ID NO:2, has at least 50% or 70%, preferably at least 85% or 90%, sequence identity with the amino acid sequence of SEQ ID NO:2, or includes a derivative of the amino acid sequence of SEQ ID NO:2, wherein the XYL-IV cleaves xylan.

[0011] Yet another embodiment of the present invention provides a method of producing XYL-IV protein including the steps of (a) obtaining a host cell which has been transformed with a vector including DNA encoding a XYL-IV protein; (b) culturing the host cell under conditions suitable for the expression and, optionally, secretion, of the XYL-IV protein; and (c) recovering the fermentation broth containing the XYL-IV protein.

[0012] In another embodiment, the invention provides an antibody which specifically binds to a XYL-IV protein or a domain thereof. Optionally, the antibody is a monoclonal antibody. In a still further embodiment, the invention provides methods using the XYL-IV protein or DNA encoding the XYL-IV protein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0013]FIG. 1 illustrates the nucleotide sequence (SEQ ID NO: 1) of a cDNA clone obtained from Trichoderma reesei RNA after growth on a mixed carbon source.

[0014]FIG. 2 illustrates the predicted amino acid sequence (SEQ ID NO:2) for a novel XYL-IV from Trichoderma reesei.

[0015]FIG. 3 illustrates locations of restriction enzyme cleavage sites along the nucleotide sequence of FIG. 1 (SEQ ID NO: 1).

[0016]FIG. 4 illustrates efficient hydrolysis of HexA³Xyl₃. Values were taken from Table 5.

[0017]FIG. 5 illustrates production of reducing sugars by XYL-IV from xylan, MeGlcA-xylan, and arabinoxylan from rye. Each xylan was present at 5 g/L and the reaction was run at 40° C. and pH 4.

[0018]FIGS. 6a and 6 b illustrate synergism of XYL-IV with each of XYL-I and -II. Product was measured as reducing sugar (FIG. 6a) and free xylose (FIG. 6b). Values were taken from Table 6.

[0019]FIGS. 7a-d illustrate synergism in stepwise action of XYL-I and XYL-IV. In FIGS. 7a and 7 b the substrate was MeGlcA-xylan. In FIGS. 7c and 7 d the substrate was rye arabinoxylan. Values were taken from Table 7.

DETAILED DESCRIPTION OF THE INVENTION

[0020] Definitions

[0021] It should be noted that, as used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to a composition containing “a compound” includes a mixture of two or more compounds. It should also be noted that the term “or” is generally employed in its sense including “and/or” unless the content clearly dictates otherwise.

[0022] “Xylanase” means a protein or polypeptide domain of a protein or polypeptide derived from a microorganism, e.g. a fungus, bacterium, or from a plant or animal, and that has the ability to catalyze cleavage of xylan at one or more of various positions of xylan's carbohydrate backbone, including branched xylans and xylooligosaccharides. Under certain conditions, a xylanase can also catalyze synthesis of a sugar such as a xylan or xylooligosaccharide from smaller units. Three specific xylanases from T. reesei are known in the literature.

[0023] As used herein, “XYL-IV” refers to an enzyme having xylanase activity and that, typically, in its native or wild type form, lacks a cellulose binding domain. The XYL-IV of the invention includes the protein including residues 1 to 465 of FIG. 2 (SEQ ID NO:2), proteins having at least 50% or 70%, preferably at least 85% or 90%, sequence identity with the amino acid sequence of SEQ ID NO:2, or a derivative of the amino acid sequence of SEQ ID NO:2, wherein the XYL-IV cleaves xylan. The XYL-UV provided by the invention specifically excludes the three known xylanases of T. reesei, which are referred to as XYL-I, XYL-II (belonging to glycosyl hydrolase family 11), and XYL-III (belonging to glycosyl hydrolase family 10) and are described in Törrönen, et al. and Xu, et al., supra). It is believed that XYL-IV acts on xylan in a different manner than the three known T. reesei xylanases, but may also cleave certain of the same positions.

[0024] It is contemplated herein that XYL-IV may be derived from any of a variety of sources including a microorganism, e.g. a fungus or a bacterium, a plant, or an animal. Specifically, it is contemplated that microorganisms which possess cellulolytic capabilities will be excellent sources of XYL-IV protein. In a particularly preferred embodiment of the invention, the XYL-IV is derived from Trichoderma spp., particularly Trichoderma reesei. However, also preferably, the XYL-IV and/or DNA encoding XYL-IV according to the present invention is derived from a fungus, such as, Absidia spp.; Acremonium spp.; Agaricus spp.; Anaeromyces spp.; Aspergillus spp., including A. aculeatus, A. awamori, A. flavus, A. foetidus, A. fumaricus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus and A. versicolor; Aeurobasidium spp.; Cephalosporum spp.; Chaetomium spp.; Coprinus spp.; Dactyllum spp.; Fusarium spp., including F. conglomerans, F. decemcellulare, F. javanicum, F. lini, F. oxysporum and F. solani; Gliocladium spp.; Humicola spp., including H. insolens and H. lanuginosa; Mucor spp.; Neurospora spp., including N. crassa and N. sitophila; Neocallimastix spp.; Orpinomyces spp.; Penicillium spp; Phanerochaete spp.; Phlebia spp.; Piromyces spp.; Rhizopus spp.; Schizophyllum spp.; Trametes spp.; Trichoderma spp., including T reesei, T. reesei (longibrachiatum) and T. viride; and Zygorhynchus spp.

[0025] Preferably, XYL-IV proteins according to the present invention are isolated or purified. By purification or isolation is meant the XYL-IV protein is altered from its natural state by virtue of separating the XYL-IV from some or all of the naturally occurring constituents with which it is associated in nature. Such isolation or purification may be accomplished by art recognized separation techniques such as ion exchange chromatography, affinity chromatography, hydrophobic separation, dialysis, protease treatment, ammonium sulphate precipitation or other protein salt precipitation, centrifugation, size exclusion chromatography, filtration, microfiltration, gel electrophoresis or separation on a gradient to remove whole cells, cell debris, impurities, extraneous proteins, or enzymes undesired in the final composition. It is further possible to then add constituents to the XYL-IV containing composition which provide additional benefits, for example, activating agents, anti-inhibition agents, desirable ions, compounds to control pH or other enzymes. Preferably, XYL-IV proteins according to the present invention are produced by recombinant methods.

[0026] As used herein, “microorganism” refers to a bacterium, a fungus, a virus, a protozoan, and other microbes or microscopic organisms. As used herein, “plant” refers to any member of the kingdom Plantae. As used herein, “animal” refers to any member of the kingdom Animalia. Animals can be either single celled or multicellular.

[0027] As used herein, “derivative” means a protein which is derived from a precursor protein (e.g., the native protein) by addition of one or more amino acids to either or both the C- and N-terminal end, substitution of one or more amino acids at one or a number of different sites in the amino acid sequence, deletion of one or more amino acids at either or both ends of the protein or at one or more sites in the amino acid sequence, or insertion of one or more amino acids at one or more sites in the amino acid sequence. The preparation of a XYL-IV derivative is preferably achieved by modifying a DNA sequence which encodes the native protein, transformation of that DNA sequence into a suitable host, and expression of the modified DNA sequence to form the derivative XYL-IV.

[0028] “Derivatives” of the invention include peptides including altered amino acid sequences in comparison with a precursor amino acid sequence (e.g., a wild type or native state XYL-IV), wherein the peptides retain a characteristic XYL-IV nature of the precursor XYL-IV but have altered properties in some specific aspect. For example, a XYL-IV derivative may have an increased pH optimum or increased temperature or oxidative stability but retains its characteristic xylan modification activity. Similarly, derivatives according to the present invention include a cellulose binding domain which has either been added, removed or modified in such a way so as to significantly impair or enhance its cellulose binding ability. A derivative according to the present invention includes a xylan, or other substrate, binding domain, which has been added or modified to alter its substrate binding ability. It is contemplated that derivatives according to the present invention are derived from a DNA fragment encoding a XYL-IV derivative wherein the functional activity of the expressed XYL-IV derivative is retained. Derivatives farther include chemical modifications that change the characteristics of the XYL-IV.

[0029] Ordinarily, a XYL-IV derivative will have at least about 50%, 70%, or 85% amino acid sequence identity, preferably at least about 85% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity, even more preferably at least about 95% amino acid sequence identity and yet more preferably 98% amino acid sequence identity with the amino acid sequence of FIG. 2 (SEQ ID NO:2). Preferably, any amino acid substitutions are “conservative amino acid substitutions” using L-amino acids, wherein one amino acid is replaced by another biologically similar amino acid. Conservative amino acid substitutions are those that preserve the general charge, hydrophobicity/hydrophilicity, and/or steric bulk of the amino acid being substituted. Examples of conservative substitutions are those between the following groups: Gly/Ala, Val/Ile/Leu, Lys/Arg, Asn/Gln, Glu/Asp, Ser/Cys/Thr, and Phe/Trp/Tyr. A derivative may, for example, differ by as few as 1 to 10 amino acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.

[0030] As used herein, a “native sequence XYL-IV” includes a polypeptide having the same amino acid sequence as a XYL-IV derived from nature. Such a native sequence XYL-IV can be isolated from nature or can be produced by recombinant or synthetic means. The term “native sequence XYL-IV” specifically encompasses naturally-occurring truncated or secreted forms of a XYL-UV and naturally-occurring variant forms (e.g., alternatively spliced forms) of a XYL-IV. In one embodiment of the invention, the native sequence XYL-IV includes amino acids 1 to 465 of FIG. 2 (SEQ ID NO:2).

[0031] As used herein, “percent (%) sequence identity” with respect to the amino acid or nucleotides sequences identified herein is defined as the percentage of amino acid residues or nucleotides in a candidate sequence that are identical with the amino acid residues or nucleotides in a XYL-IV sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.

[0032] Methods for performing sequence alignment and determining sequence identity are known to the skilled artisan, may be performed without undue experimentation, and calculations of identity values may be obtained with definiteness. See, for example, Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 19 (Greene Publishing and Wiley-Interscience, New York); and the ALIGN program (Dayhoff (1978) in Atlas of Protein Sequence and Structure 5:Suppl. 3 (National Biomedical Research Foundation, Washington, D.C.). A number of algorithms are available for aligning sequences and determining sequence identity and include, for example, the homology alignment algorithm of Needleman et al. (1970) J. Mol. Biol. 48:443; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the search for similarity method of Pearson et al. (1988) Proc. Natl. Acad. Sci. 85:2444; the Smith-Waterman algorithm (Meth. Mol. Biol. 70:173-187 (1997); and BLASTP, BLASTN, and BLASTX algorithms (see Altschul et al. (1990) J. Mol. Biol. 215:403-410). Computerized programs using these algorithms are also available, and include, but are not limited to: ALIGN or Megalign (DNASTAR) software, or WU-BLAST-2 (Altschul et al., Meth. Enzym., 266:460-480 (1996)); or GAP, BESTFIT, BLAST Altschul et al., supra, FASTA, and TFASTA, available in the Genetics Computing Group (GCG) package, Version 8, Madison, Wis., USA; and CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, Calif. Those skilled in the art can determine appropriate parameters for measuring alignment, including algorithms needed to achieve maximal alignment over the length of the sequences being compared. Preferably, the sequence identity is determined using the default parameters determined by the program. Specifically, sequence identity can be determined by the Smith-Waterman homology search algorithm (Meth. Mol. Biol. 70:173-187 (1997)) as implemented in MSPRCH program (Oxford Molecular) using an affine gap search with the following search parameters: gap open penalty of 12, and gap extension penalty of 1. Preferably, paired amino acid comparisons can be carried out using the GAP program of the GCG sequence analysis software package of Genetics Computer Group, Inc., Madison, Wis., employing the blosum62 amino acid substitution matrix, with a gap weight of 12 and a length weight of 2.

[0033] With respect to optimal alignment of two amino acid sequences, the contiguous segment of the variant amino acid sequence may have additional amino acid residues or deleted amino acid residues with respect to the reference amino acid sequence. The contiguous segment used for comparison to the reference amino acid sequence will include at least 20 contiguous amino acid residues, and may be 30, 40, 50, or more amino acid residues. Corrections for increased sequence identity associated with inclusion of gaps in the derivative's amino acid sequence can be made by assigning gap penalties.

[0034] As used herein, “expression vector” means a DNA construct including a DNA sequence which is operably linked to a suitable control sequence capable of affecting the expression of the DNA in a suitable host. Such control sequences may include a promoter to affect transcription, an optional operator sequence to control transcription, a sequence encoding suitable ribosome-binding sites on the mRNA, and sequences which control termination of transcription and translation. Different cell types are preferably used with different expression vectors. A preferred promoter for vectors used in Bacillus subtilis is the AprE promoter; a preferred promoter used in E. coli is the Lac promoter, a preferred promoter used in Saccharomyces cerevisiae is PGK1, a preferred promoter used in Aspergillus niger is glaA, and a preferred promoter for Trichoderma reesei is cbhI. The vector may be a plasmid, a phage particle, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, under suitable conditions, integrate into the genome itself. In the present specification, plasmid and vector are sometimes used interchangeably. However, the invention is intended to include other forms of expression vectors which serve equivalent functions and which are, or become, known in the art. Thus, a wide variety of host/expression vector combinations may be employed in expressing the DNA sequences of this invention. Useful expression vectors, for example, may consist of segments of chromosomal, non-chromosomal and synthetic DNA sequences such as various known derivatives of SV40 and known bacterial plasmids, e.g., plasmids from E. coli including col E1, pCR1, pBR322, pMb9, pUC 19 and their derivatives, wider host range plasmids, e.g., RP4, phage DNAs e.g., the numerous derivatives of phage λ, e.g., NM989, and other DNA phages, e.g., M13 and filamentous single stranded DNA phages, yeast plasmids such as the 2μ plasmid or derivatives thereof, vectors useful in eukaryotic cells, such as vectors useful in animal cells and vectors derived from combinations of plasmids and phage DNAs, such as plasmids which have been modified to employ phage DNA or other expression control sequences. Expression techniques using the expression vectors of the present invention are known in the art and are described generally in, for example, Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL, SECOND EDITION, Cold Spring Harbor Press (1989). Often, such expression vectors including the DNA sequences of the invention are transformed into a unicellular host by direct insertion into the genome of a particular species through an integration event (see e.g., Bennett & Lasure, MORE GENE MANIPULATIONS IN FUNGI, Academic Press, San Diego, pp. 70-76 (1991) and articles cited therein describing targeted genomic insertion in fungal hosts).

[0035] As used herein, “host strain” or “host cell” means a suitable host for an expression vector including DNA according to the present invention. Host cells useful in the present invention are generally prokaryotic or eukaryotic hosts, including any transformable microorganism in which expression can be achieved. Specifically, host strains may be Bacillus subtilis, Escherichia coli, Trichoderma reesei, Saccharomyces cerevisiae or Aspergillus niger. Host cells are transformed or transfected with vectors constructed using recombinant DNA techniques. Such transformed host cells are capable of both replicating vectors encoding XYL-IV and its derivatives or variants (mutants) or expressing the desired peptide product. In a preferred embodiment according to the present invention, “host cell” means both the cells and protoplasts created from the cells of Trichoderma sp.

[0036] As used herein, “signal sequence” means a sequence of amino acids bound to the N-terminal portion of a protein which facilitates the secretion of the mature form of the protein outside of the cell. This definition of a signal sequence is a functional one. The mature form of the extracellular protein lacks the signal sequence which is cleaved off during the secretion process.

[0037] As used herein, “functionally attached” or “operably linked” means that a regulatory region, such as a promoter, terminator, secretion signal or enhancer region is attached to or linked to a structural gene and controls the expression of that gene.

[0038] “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology (Wiley Interscience Publishers, 1995).

[0039] As used herein, “stringent conditions” or “high-stringency conditions” can be identified by those that: (1) employ low ionic strength and high temperature for washing, for example, 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5× SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2× SSC (sodium chloride/sodium citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1× SSC containing EDTA at 55° C.

[0040] As used herein, “moderately-stringent conditions” can be identified as described by Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Press, 1989), and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength, and %SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5× SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1× SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

[0041] As used herein, a substance (e.g. a polynucleotide or protein) “derived from” a microorganism means that the substance is native to the microorganism.

[0042] XYL-IV Specificity

[0043] In general, XYL-UV exhibits specificity different from that of a family 11 or a family 10 glycosyl hydrolase. In particular, XYL-IV exhibits specificity for substrates different from that of an α-arabinofuranosidase, an α-galactosidase, a β-xylosidase, a β-mannosidase. More particularly, XYL-IV cleaves substrates with a specificity different from XYL-I or -II or -III, That is, XYL-IV may cleave xylan at some of the same positions as these other xylanases, but it also cleaves at different positions.

[0044] In one embodiment, under typical reaction conditions, XYL-IV can exhibit greater activity toward an unsubstituted xylan or an acetylated MeGIcA-xylan, than do XYL-I or XYL-II. Both XYLs-IV and -II can hydrolyze deacetylated MeGlcA-xylan. XYL-II typically exhibits greater activity than XYL-IV toward an arabinoxylan. In cleavage of unsubstituted xylan or an acetylated MeGlcA-xylan, XYL-IV produced xylose as its main product, with lesser amounts of xylobiose and substituted xylooligosaccharides. The other two xylanases made different products. XYL-IV will generally cleave closer to a substituted xylose unit than either XYL-I or -II.

[0045] The difference in specificity between XYL-IV and XYLs-I and -II can yield synergy in cleavage of a product by combinations or mixtures of these enzymes. For example, cleavage of a substrate by a mixture of XYL-IV with XYL-I and/or XYL-H can result in a more than additive increase in the rate and/or extent of cleavage of the substrate compared to cleavage by fewer of these enzymes. Similarly, cleavage of a substrate by one or more of XYLs-I, -II and/or -IV followed by cleavage by a different XYL or combination of XYL-I, -II and/or -IV can result in a more than additive increase in the rate and/or extent of cleavage of the substrate compared to cleavage by fewer of these enzymes.

[0046] In one embodiment, XYL-IV can cleave several polymeric xylans from rye, unsubstituted xylan, MeGlcA-xylan, and arabinoxylan. Typically, XYL-IV cleaves arabinoxylan more slowly than the other two xylans, which can be cleaved at approximately equal rates. XYL-IV can hydrolyze both linear and substituted oligosaccharides. XYL-IV, under typical reaction conditions, does not cleave, or cleaves only poorly a glucomannan, a galactomannan, a β-glucan, a carboxymethyl cellulose, a laminarin, or a xylobiose.

[0047] In another embodiment, XYL-IV can be employed under certain reaction conditions to catalyze the coupling of sugars to form larger sugars. For example, XYL-IV can be employed for synthesis of a xylobiose or a xylooligosaccharide from smaller units. Alternatively, XYL-IV can catalyze formation of sugar derivatives from smaller units.

[0048] Preparation of XYL-IV

[0049] The present invention relates to the expression, isolation and use of XYL-IV and derivatives of XYL-IV. The XYL-IV or derivative is preferably prepared by recombinant methods. However, XYL-IV proteins for use in the present invention may be obtained by other art recognized means such as purification from natural isolates or chemical synthesis.

[0050] Purification from Natural Isolates

[0051] XYL-UV can be purified from natural isolates by known and commonly employed methods. For example, cells containing XYL-IV can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents. The XYL-IV can be recovered from the medium by conventional techniques including separations of the cells from the medium by centrifugation, filtration, and precipitation of the proteins in the supernatant or filtrate with a salt, for example, ammonium sulphate. The XYL-IV can then be purified from the disrupted cells by procedures such as: fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica-based materials or on a ion-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; and affinity chromatography. Various methods of protein purification may be employed and such methods are known in the art and described for example in Deutscher, Methods in Enzymology 182 (1990); Scopes, PROTEIN PURIFICATION: PRINCIPLES AND PRACTICE, Springer-Verlag, New York (1982). The purification step(s) selected will depend, for example, on the particular XYL-IV produced or on the source of this enzyme.

[0052] Chemical Synthesis

[0053] Alternatively, the XYL-IV sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques (see, e.g., Stewart, et al., SOLID-PHASE PEPTIDE SYNTHESIS, W.H. Freeman Co., San Francisco, Calif. (1969); Merrifield, J. Am. Chem. Soc. 85:2149-2154 (1963)). In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City, Calif.) using manufacturer's instructions. Various portions of XYL-IVs may be chemically synthesized separately and combined using chemical or enzymatic methods to produce a full-length XYL-IV.

[0054] Recombinant Methods

[0055] Isolation of DNA Encoding the XYL-IV

[0056] DNA encoding a XYL-IV may be obtained from a cDNA library prepared from a microorganism believed to possess the XYL-IV mRNA and to express it at a detectable level. The XYL-IV-encoding gene may also be obtained from a genomic library or by oligonucleotide synthesis.

[0057] Libraries can be screened with probes (such as antibodies to a XYL-IV or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook, et al., supra. An alternative means to isolate the gene encoding XYL-IV is to use PCR methodology (Sambrook, et al., supra; Dieffenbach, et al., PCR PRIMER: A LABORATORY MANUAL (Cold Spring Harbor Laboratory Press, 1995)).

[0058] In known techniques for screening a cDNA library, the oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized. The oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like ³²P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook, et al., supra.

[0059] Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined through sequence alignment using computer software programs such as ALIGN, DNAstar, and INHERIT, which employ various algorithms to measure homology.

[0060] Nucleic acid having a protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook, et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.

[0061] Selection and Transformation of Host Cells

[0062] Host cells are transfected or transformed with expression or cloning vectors described herein for XYL-UV production. The host cells are cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. The culture conditions, such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in MAMMALIAN CELL BIOTECHNOLOGY: A PRACTICAL APPROACH, M. Butler, ed. (IRL Press, 1991) and Sambrook, et al., supra.

[0063] Methods of transfection are known to the ordinarily skilled artisan, for example, CaPO₄ and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook, et al., supra, or electroporation is generally used for prokaryotes or other cells that contain substantial cell-wall barriers. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw, et al., Gene 23:315 (1983) and WO 89/05859 published Jun. 29, 1989. Transformations into yeast can be carried out according to the method of Van Solingen, et al., J. Bacteriol. 130:946 (1977) and Hsiao, et al., Proc. Nat'l Acad. Sci. (USA) 76:3829 (1979). However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, microporation, biolistic bombardment, bacterial protoplast fusion with intact cells, or polycations, e.g. polybrene, polyornithine, may also be used.

[0064] Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or filamentous fungal cells. Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W31 10 (ATCC 27,325) and K5 772 (ATCC 53,635). In addition to prokaryotes, eukaryotic microorganisms such as filamentous fungi or yeast are suitable cloning or expression hosts for vectors encoding XYL-IV. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.

[0065] Preferably, the microorganism to be transformed includes a strain derived from Trichoderma spp. or Aspergillus spp. More preferably, the strain includes T. reesei which is useful for obtaining overexpressed protein or Aspergillus niger var. awamori. For example, Trichoderma strain RL-P37, described by Sheir-Neiss, et al. in Appl. Microbiol. Biotechnol. 20:46 (1984) is known to secrete elevated amounts of cellulase enzymes. Functional equivalents of RL-P37 include Trichoderma reesei (longibrachiatum) strain RUT-C30 (ATCC No. 56765) and strain QM9414 (ATCC No. 26921). Another example includes overproducing mutants as described in Ward, et al. in Appl. Microbiol. Biotechnol. 39:738 (1993). It is contemplated that these strains would also be useful in overexpressing Trichoderm spp. XYL-IV. The selection of the appropriate host cell is deemed to be within the skill in the art.

[0066] Selection and Transformation of Trichoderma sp. Host Cells

[0067] A preferred mode for preparing XYL-IV according to the present invention includes transforming a Trichoderma sp. host cell with a DNA construct including at least a fragment of DNA encoding a portion or all of the XYL-IV functionally attached to a promoter. The transformed host cell is then grown under conditions so as to express the desired protein. Subsequently, the desired protein product can be isolated or purified to substantial homogeneity.

[0068] Preferably, the microorganism to be transformed includes a strain derived from Trichoderma spp. More preferably, the strain includes T. reesei which is useful for obtaining overexpressed protein, Trichoderma strain RL-P37, functional equivalents of RL-P37, such as Trichoderma reesei (longibrachiatum) strain RUT-C30 (ATCC No. 56765), or strain QM9414 (ATCC No. 26921).

[0069] A selectable marker must be chosen so as to enable detection of the transformed fungus. Any selectable marker gene which is expressed in the selected microorganism will be suitable. For example, with Trichoderma sp., the selectable marker is chosen so that the presence of the selectable marker in the transformants will not significantly affect the properties thereof. Such a selectable marker may be a gene which encodes an assayable product. For example, a functional copy of a Trichoderma sp. gene may be used which if lacking in the host strain results in the host strain displaying an auxotrophic phenotype.

[0070] In a preferred embodiment, a pyr4⁻ derivative strain of Trichoderma sp. is transformed with a functional pyr4 gene, which thus provides a selectable marker for transformation. A pyr4⁻ derivative strain may be obtained by selection of Trichoderma sp. strains which are resistant to fluoroorotic acid (FOA). The pyr4 gene encodes orotidine-5′-monophosphate decarboxylase, an enzyme required for the biosynthesis of uridine. Strains with an intact pyr4 gene grow in a medium lacking uridine but are sensitive to fluoroorotic acid. It is possible to select pyr4⁻ derivative strains which lack a functional orotidine monophosphate decarboxylase enzyme and require uridine for growth by selecting for FOA resistance. Using the FOA selection technique it is also possible to obtain uridine requiring strains which lack a functional orotate pyrophosphoribosyl transferase. It is possible to transform these cells with a functional copy of the gene encoding this enzyme (Berges and Barreau, Curr. Genet. 19:359 (1991)). Selection of derivative strains is easily performed using the FOA resistance technique referred to above, and thus, the pyr4 gene is preferably employed as a selectable marker.

[0071] To transform pyr4⁻ Trichoderma sp. so as to have the ability to express one or more xyl4 genes, a single DNA fragment including a xyl4 gene is then isolated from the deletion plasmid and used to transform an appropriate pyr⁻ Trichoderma host. Transformants are then identified and selected based on their ability to express the pyr4 gene product and thus compliment the uridine auxotrophy of the host strain. Southern blot analysis is then carried out on the resultant transformants to identify and confirm a double crossover integration event which replaces part or all of the coding region of the genomic copy of the gene to be deleted with the pyr4 selectable markers.

[0072] Although the specific plasmid vectors described above relate to preparation of pyr⁻ transformants, the present invention is not limited to these vectors. Various genes can be deleted and replaced in the Trichoderma sp. strain using the above techniques. In addition, any available selectable markers can be used, as discussed above. In fact, any Trichoderma sp. gene which has been cloned, and thus identified, can be deleted from or replaced in the genome using the above-described strategy.

[0073] As stated above, preferred host strains include derivatives of Trichoderma sp. which lack or have a nonfunctional gene or genes corresponding to the selectable marker chosen. For example, if the selectable marker of pyr4 is chosen, then a specific pyr4⁻ derivative strain is used as a recipient in the transformation procedure. Similarly, selectable markers including Trichoderma sp. genes equivalent to the Aspergillus nidulans genes amdS, argB, trpC, niaD may be used. The corresponding recipient strain must therefore be a derivative strain such as argB⁻, trpC⁻, niaD⁻, respectively.

[0074] In the preferred transformation technique, it must be taken into account that the permeability of the cell wall to DNA in Trichoderma sp. is very low. Accordingly, uptake of the desired DNA sequence, gene or gene fragment is at best minimal. There are a number of methods to increase the permeability of the Trichoderma sp. cell wall in the derivative strain (i.e., lacking a functional gene corresponding to the used selectable marker) prior to the transformation process.

[0075] The preferred method in the present invention to prepare Trichoderma sp. for transformation involves the preparation of protoplasts from fungal mycelium. The mycelium can be obtained from germinated vegetative spores. The mycelium is treated with an enzyme which digests the cell wall resulting in protoplasts. The protoplasts are then protected by the presence of an osmotic stabilizer in the suspending medium. These stabilizers include sorbitol, mannitol, potassium chloride, magnesium sulfate and the like. Usually the concentration of these stabilizers varies between 0.8 M to 1.2 M. It is preferable to use about a 1.2 M solution of sorbitol in the suspension medium.

[0076] Uptake of the DNA into the host Trichoderma sp. strain is dependent upon the calcium ion concentration. Generally between about 10 mM CaCl₂ and 50 mM CaCl₂ is used in an uptake solution. Besides the need for the calcium ion in the uptake solution, other items generally included are a buffering system such as TE buffer (10 Mm Tris, pH 7.4; 1 mM EDTA) or 10 mM MOPS, pH 6.0 buffer (morpholinepropanesulfonic acid) and polyethylene glycol (PEG). It is believed that the polyethylene glycol acts to fuse the cell membranes thus permitting the contents of the medium to be delivered into the cytoplasm of the Trichoderma sp. strain and the plasmid DNA is transferred to the nucleus. This fusion frequently leaves multiple copies of the plasmid DNA tandemly integrated into the host chromosome.

[0077] Usually a suspension containing the Trichoderma sp. protoplasts or cells that have been subjected to a permeability treatment at a density of 10⁸ to 10⁹/ml, preferably 2×10⁸/ml are used in transformation. A volume of 100 microliters of these protoplasts or cells in an appropriate solution (e.g., 1.2 M sorbitol; 50 mM CaCl₂) are mixed with the desired DNA. Generally a high concentration of PEG is added to the uptake solution. From 0.1 to 1 volume of 25% PEG 4000 can be added to the protoplast suspension. However, it is preferable to add about 0.25 volumes to the protoplast suspension. Additives such as dimethyl sulfoxide, heparin, spermidine, potassium chloride and the like may also be added to the uptake solution and aid in transformation.

[0078] Generally, the mixture is then incubated at approximately 0° C. for a period of between 10 to 30 minutes. Additional PEG is then added to the mixture to further enhance the uptake of the desired gene or DNA sequence. The 25% PEG 4000 is generally added in volumes of 5 to 15 times the volume of the transformation mixture; however, greater and lesser volumes may be suitable. The 25% PEG 4000 is preferably about 10 times the volume of the transformation mixture. After the PEG is added, the transformation mixture is then incubated at room temperature before the addition of a sorbitol and CaCl₂ solution. The protoplast suspension is then further added to molten aliquots of a growth medium. This growth medium permits the growth of transformants only. Any growth medium can be used in the present invention that is suitable to grow the desired transformants. However, if Pyr⁺ transformants are being selected it is preferable to use a growth medium that contains no uridine. The subsequent colonies are transferred and purified on a growth medium depleted of uridine.

[0079] At this stage, stable transformants may be distinguished from unstable transformants by their faster growth rate and the formation of circular colonies with a smooth, rather than ragged outline on solid culture medium lacking uridine. Additionally, in some cases a further test of stability may made by growing the transformants on solid non-selective medium (i.e. containing uridine), harvesting spores from this culture medium and determining the percentage of these spores which will subsequently germinate and grow on selective medium lacking uridine.

[0080] Preparation and Use of a Replicable Vector

[0081] DNA encoding the XYL-IV protein is prepared for insertion into an appropriate microorganism. According to the present invention, DNA encoding for a XYL-IV enzyme includes all of the DNA necessary to encode for a protein which has functional XYL-IV activity. Accordingly, DNA may be derived from any microbial source which produces XYL-IV, provided that the gene may be identified and isolated pursuant to the methods described herein. In a preferred embodiment, the DNA encodes for an XYL-IV protein derived from Trichoderma sp., and more preferably from Trichoderma reesei.

[0082] The DNA encoding the XYL-IV may be prepared by the construction of an expression vector carrying the DNA encoding the XYL-IV. The expression vector carrying the inserted DNA fragment encoding the XYL-IV may be any vector which is capable of replicating autonomously in a given host organism or of integrating into the DNA of the host, typically a plasmid, cosmid, viral particle, or phage. Various vectors are publicly available. It is also contemplated that more than one copy of DNA encoding a XYL-IV may be recombined into the strain to facilitate overexpression.

[0083] In preferred embodiments two types of expression vectors for obtaining expression of genes are contemplated. The first contains DNA sequences in which the promoter, gene coding region, and terminator sequence all originate from the gene to be expressed. Gene truncation may be obtained by deleting away undesired DNA sequences (e.g., coding for unwanted domains) to leave the domain to be expressed under control of its own transcriptional and translational regulatory sequences. A selectable marker is also contained on the vector allowing the selection for integration into the host of multiple copies of the novel xyl4 gene sequences.

[0084] The second type of expression vector is preassembled and contains sequences required for high level transcription and a selectable marker. It is contemplated that the coding region for a gene or part thereof can be inserted into this general purpose expression vector such that it is under the transcriptional control of the expression cassette's promoter and terminator sequences. For example, pTEX is such a general purpose expression vector. See U.S. Pat. No. 5,650,322 for a description of this vector. pTEX is a plasmid that has been designed as a multi-purpose expression vector for use in the filamentous fungus T. reesei. The expression cassette within the vector has several unique features that make it useful for this function. Transcription is regulated using the strong cbh1 gene promoter and terminator sequences for T. reesei.

[0085] In the vector, the DNA sequence encoding the XYL-IV of the present invention should be operably linked to transcriptional and translational sequences, i.e., a suitable promoter sequence and signal sequence in reading frame to the structural gene. The promoter may be any DNA sequence which shows transcriptional activity in the host cell and may be derived from genes encoding proteins either homologous or heterologous to the host cell. The signal peptide provides for extracellular production of the XYL-IV or derivatives thereof. The DNA encoding the signal sequence is preferably that which is naturally associated with the gene to be expressed, however the signal sequence from any suitable source, for example an exo-cellobiohydrolases or endoglucanase from Trichoderma, is contemplated in the present invention.

[0086] The appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan.

[0087] The desired XYL-IV may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide. In general, the signal sequence may be a component of the vector or it may be a part of the XYL-IV-encoding DNA that is inserted into the vector. The signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces α-factor leaders, the latter described in U.S. Pat. No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179 published Apr. 4, 1990), or the signal described in WO 90/13646 published Nov. 15, 1990.

[0088] Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria and the 2μ plasmid origin is suitable for yeast.

[0089] Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli. A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7 (Stinchcomb, et al., Nature 282:39 (1979); Kingsman, et al., Gene 7:141 (1979); Tschemper, et al., Gene 10:157 (1980)). The trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 (Jones, Genetics 85:12 (1977)). A preferred selection gene for use in Trichoderma sp is the pyr4 gene.

[0090] Expression and cloning vectors usually contain a promoter operably linked to the XYL-IV-encoding nucleic acid sequence. The promoter directs mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Preferred promoters include a fungal promoter sequence, for example, the promoter of the cbh1 or egl1 gene.

[0091] Promoters suitable for use with prokaryotic hosts include the β-lactamase and lactose promoter systems (Chang, et al., Nature 275:615 (1978); Goeddel, et al., Nature, 281:544 (1979)), alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucl. Acids Res. 8:4057 (1980); and European patent application 36,776), and hybrid promoters such as the tac promoter (deBoer, et al., Proc. Nat'l Acad. Sci. USA 80:21 (1983)). Promoters for use in bacterial systems also will contain a Shine-Dalgamo (S.D.) sequence operably linked to the DNA encoding the XYL-IV.

[0092] Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase (Hitzeman, et al., J. Biol. Chem. 255:2073 (1980)) or other glycolytic enzymes (Hess, et al., J. Adv. Enzyme Reg. 7:149 (1968); Holland, Biochem. 17:4900 (1978)), such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase. Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.

[0093] Expression vectors used in eukaryotic host cells (e.g., yeast, fungi, insect, plant) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding XYL-IV.

[0094] Detecting Gene Amplification/Expression

[0095] Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA (Thomas, Proc. Nat'l Acad. Sci. USA 77:5201 (1980)), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

[0096] Gene expression, alternatively, may be measured by immunological methods, such as immunohistochemical staining of cells and assay of cell culture fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence XYL-IV, against a synthetic peptide based on the DNA sequences provided herein, or against an exogenous sequence fused to XYL-IV-encoding DNA and encoding a specific antibody epitope.

[0097] Polypeptide Purification

[0098] Forms of XYL-IV may be recovered from culture medium or from host cell lysates by the methods described above for isolation and purification from natural isolates. Additional techniques can be used depending on the host cell employed and any variant structures in the recombinant enzyme. For example, if the recombinant enzyme is membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Purification of recombinant enzyme may also employ protein A Sepharose columns to remove contaminants such as IgG and metal chelating columns to bind epitope-tagged forms of the XYL-IV. The purification step(s) selected will depend, for example, on the nature of the production process used, the particular XYL-IV produced, and any variant structure for the recombinant enzyme.

[0099] Derivatives of XYL-IV

[0100] In addition to the native sequence XYL-IV described herein, it is contemplated that XYL-IV derivatives can be prepared with altered amino acid sequences. XYL-IV derivatives can be prepared by introducing appropriate nucleotide changes into the XYL-IV-encoding DNA, or by synthesis of the desired XYL-IV. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of the XYL-IV, such as changing the number or position of glycosylation sites.

[0101] Derivatives of the native sequence XYL-IV or of various domains of the XYL-IV described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Pat. No. 5,364,934. Sequence variations may be a substitution, deletion or insertion of one or more codons encoding the XYL-IV that results in a change in the amino acid sequence of the XYL-IV as compared with the native sequence XYL-IV. Optionally, the sequence variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of the XYL-IV.

[0102] Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired XYL-IV activity may be found by comparing the sequence of the polypeptide with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology. Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting derivatives for functional activity using techniques known in the art.

[0103] The sequence variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter, et al., Nucl. Acids Res. 13:4331 (1986); Zoller, et al., Nucl. Acids Res. 10:6487 (1987)), cassette mutagenesis (Wells, et al., Gene 34:315 (1985)), restriction selection mutagenesis (Wells, et al., Philos. Trans. R. Soc. London SerA 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the XYL-IV-encoding DNA with a variant sequence.

[0104] Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the derivative. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, THE PROTEINS, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of derivative, an isosteric amino acid can be used.

[0105] Anti-XYL-IV Antibodies

[0106] The present invention further provides anti-XYL-IV antibodies. Exemplary antibodies include polyclonal and monoclonal antibodies.

[0107] The anti-XYL-IV antibodies of the present invention may include polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. For anti-XYL-IV antibodies, the immunizing agent may include the XYL-IV or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.

[0108] The anti-XYL-IV antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.

[0109] For anti-XYL-IV antibodies, the immunizing agent will typically include the XYL-IV or a fusion protein thereof. Generally, either peripheral blood lymphocytes (“PBLs”) are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, MONOCLONAL ANTIBODIES: PRINCIPLES AND PRACTICE, Academic Press, (1986) pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.

[0110] Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol. 133:3001 (1984); Brodeur, et al., MONOCLONAL ANTIBODY PRODUCTION TECHNIQUES AND APPLICATIONS, Marcel Dekker, Inc., New York, (1987) pp. 51-63).

[0111] The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against a XYL-IV. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem. 107:220 (1980).

[0112] After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, supra). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium.

[0113] The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

[0114] The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison, et al., supra) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

[0115] The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.

[0116] In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art.

[0117] Methods Employing XYL-IV

[0118] In another embodiment, the xylanases of the present invention have applications in enhancing the delignification and/or the bleaching of pulp according to art-recognized techniques. The process includes contacting the pulp with XYL-IV and is dependent upon factors such as pH, temperature, treatment time, dosage of enzyme and the quantity and type of pulp.

[0119] It is preferred that the above process be carried out at a temperature and pH which will enhance the enzymatic activity of the XYL-IV. The preferred treatment period for applying the XYL-IV of the present invention is from about 10 minutes to about 4 hours depending upon factors such as the results desired, the quantity and quality of pulp treated and concentration of enzyme, for example.

[0120] A suitable enzyme dose is about 0.10 to 200 units/g of dry pulp more preferably 0.50 to 50 units/g. The xylanase activity of the enzyme preparations is determined as follows: To 1.8 ml of xylan solution (0.6% Sigma No. X-0627, prepared in 0.05 M sodium acetate buffer and adjusted to pH 5.3 with acetic acid), 0.200 ml of suitably diluted enzyme in the same buffer is added. The solution is incubated at 40° C. for exactly 30 minutes. The reaction is then stopped by adding 3 ml DNS reagent (3,5-dinitrosalicylate 10 f/l; Na,K tartrate 300 g/l), and the color is developed by boiling the sample for 5 minutes. The absorbency is then measured at a wave length of 540 nm. One enzyme unit liberates one micromole of reducing sugars calculated as xylose per minute under assay conditions. The activity is calculated from an enzyme dilution liberating 4 micromoles of reducing sugar under assay conditions. The activity of XYL-IV can also be stated in mass units, for example, a preferred amount of XYL-IV can be about 1 ppm to about 100,000 ppm in an assay or reaction mixture.

[0121] The present method may be applied to upgrade or assist in the upgrading of any of a wide variety of processed pulps, i.e., pulps which have been already previously treated in any of a variety of ways to reduce their lignin content and are treated in the process to further enhance the lignin removal by chemical methods. The present method may be applied to treat hardwood and softwood kraft pulps to enhance lignin removal and brightening of the pulps. The method is particularly applicable to chemical pulps, i.e., those in which the lignin component has been chemically modified by various chemical treatments such as in the sulfate (kraft) processes and oxygen delignification, and is preferably applied to kraft pulps. In a preferred method, the XYL-IV is applied to the pulp after kraft digestion or oxygen delignification but prior to bleaching. In the case where both kraft digestion and oxygen delignification are performed on the same pulp, the enzyme is applied after kraft digestion, prior to oxygen delignification or after oxygen delignification. The present invention is also applicable to ozone bleached pulps.

[0122] The resulting pulp is treated to remove the releasable lignin component using an appropriate extractant. In another embodiment, pulp treated with the XYL-IV may be subsequently treated with lignin-degrading chemicals such as chlorine, chlorine dioxide and peroxide, and further extracted with an appropriate extractant. In yet another embodiment, the enzyme treated pulp may be treated with an appropriate extractant, followed by lignin degradation and a final treatment with an appropriate extractant. Such extractants essentially solubilize the affected lignin component and suitable extractants include but are not limited to bases such as alkali metal hydroxides (E), DMF, dioxane, acetone, and alcohol. Hydroxide extractions may be combined with hydrogen peroxide (E_(p)) or oxygen (E_(p)). The resulting pulp may then be further bleached by a chemical bleaching sequence such as chlorine dioxide (DED) or peroxide (P-P) to the desired brightness whereby substantial savings of chemicals are observed when compared to pulp bleached to the same brightness by the same sequence but without using the enzyme treatment. Reduction of chlorine containing chemicals or peroxide is achieved in such a way. In addition, by performing the present invention with the above presented enzymes, one may apply the same amount of bleaching chemicals to the pulp and yet achieve a greater brightness in the treated pulp.

[0123] In another embodiment, the present invention provides for additional applications of the XYL-IV described above in a variety of industrial settings. For example, the XYL-IV may be used to enzymatically breakdown agricultural wastes for production of alcohol fuels and other important industrial chemicals, for production of animal or human foodstuffs, or as a component in a detergent composition.

[0124] The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.

EXAMPLES Example 1 Trichoderma reesei cDNA Clone Encoding a Novel Xylanase

[0125]FIG. 1 shows the nucleotide sequence (SEQ. ID:NO 1) and predicted corresponding amino acid sequence (SEQ. ID:NO 2) of a cDNA clone obtained from a library of cDNA prepared from Trichoderma reesei RNA after growth on a mixed carbon source by methods common in the art. An open reading frame of 1518 nucleotides was identified and the encoded protein was deduced. The mature protein was predicted to be 465 amino acids in length.

[0126] The XYL-IV identified above lacks the cellulose binding domain (CBD) of some of the cellulases produced by Trichoderma and other fungal cellulases. CBDs are also associated with some non-cellulolytic extracellular fungal enzymes such as acetyl xylan esterase and mannanase from Trichoderma reesei (longibrachiatum). The XYL-IV identified above also lacks a sequence having identity with the linker or hinge regions present in Trichoderma and other fungal cellulases and which connect the CBD with the catalytic domain.

[0127] Regions with sequence identity and sequence similarity are observed between the predicted amino acid sequence (SEQ ID NO: 2) of the Trichoderma xylanase of FIG. 2 and known sequences of microbial glycosidases and certain sequences of unknown function. Identity and similarity were detected in a search of protein sequence databanks carried out with the program BLAST (Altschul, et al., J. Mol. Biol. 215:403 (1990)) or another similar program known in the art. Sequence similarity was determined by standard methods.

[0128] In particular, paired amino acid comparisons were carried out using the GAP program of the GCG sequence analysis software package of Genetics Computer Group, Inc., Madison, Wis. Sequence similarity was determined by standard methods. This analysis of the amino acid sequence of the T. reesei XYL-IV is reported in Table 1 using the GAP program with the blosum62 amino acid substitution matrix, with a gap weight of 12 and a length weight of 2.

[0129] This analysis of the amino acid sequence of the T. reesei XYL-IV is reported in Table 1. TABLE 1 Sequence Identity and Similarity Comparisons of XYL-IV Amycolatopsis orientalis Erwinia Aeromonas cosmid Bacillus subtilus chrysanthemi caviae xylanase PCZA361 genome xylanase gene D gene T. reesei 38% identity 25% identity 29% identity 23% identity xylanse-4 43% similarity 33% similarity 36% similarity 31% similarity Amycolatopsis 29% identity 24% identity 28% identity orientalis 38% similarity 33% similarity 36% similarity cosmid PCZA361 Bacillus subtilus 40% identity 77% identity genome 49% similarity 82% similarity Erwinia 41% identity chrysanthemi 49% similarity xylanase gene

Example 2 Characterization of XYL-IV

[0130] The XYL-IV, or XYL IV, was characterized by several methods common for characterizing proteins and enzymes.

[0131] The XYL-IV from Trichoderma reesei was isolated. Upon polyacrylamide gel electrophoresis, this XYL-UV shows a molecular weight of approximately 43.0 kDa. This XYL-IV has several isoforms each with a pI of approximately 7, as determined by PHAST® system (Pharmacia). Slight staining by Schiff's reagent indicates only a low level of glycosylation. The XYL-IV gene was expressed when the Trichoderma reesei was grown on cellulose as the sole carbon source, but not when grown on glucose as the sole carbon source.

[0132] What is believed to be an N-terminal amino acid sequence of the mature XYL-IV was determined by Edman degradation after trypsin cleavage of the protein and isolation of peptides by C18 reverse phase HPLC. The N-terminal sequence was determined as: Xaa-Ser-Tyr-Ala-Thr-Xaa-Ser-Gln-Tyr-Xaa-Ala-Asn-Ile-Xaa-Ile- in which Xaa indicates an amino acid that remained unidentified due to insufficient signal.

[0133] XYL IV is homologous to xylanases that are classified as belonging to Family 5 of glycosyl hydrolases.

[0134] Employing a xylan substrate, which may not be the optimal substrate for XYL-IV, the pH optimum of XYL-IV activity was observed to be between pH 3.5 and 4. This differs from the pH optima for XYL-II, pH 5-5.5, and XYL 1, pH 3.5-4.5. At pH 4, XYL-IV showed highest activity levels at temperatures between 40 and 50° C. This enzyme retained activity in solution at room temperature for several hours, but slowly lost activity at elevated temperatures.

[0135] Substrate specificity of XYL-IV was determined for macromolecular substrates and p-nitrophenyl-glycosides. The following macromolecular substances were not significantly cleaved by XYL-IV after 24 hr at 40° C. at pH 4 in a sodium citrate buffer: glucomannan (konjac, Megazyme), galactomannan (locust bean, Sigma), β-glucan (barley, Megazyme), carboxymethyl cellulose (Fluka), laminarin (Sigma) or xylobiose. Employing known p-nitrophenyl-glycoside substrates, XYL-IV did not show activity expected for an α-arabinofuranosidase, an α-galactosidase, a β-xylosidase, or a β-mannosidase.

[0136] The XYL-IV was further evaluated for hydrolysis of several substrates in the presence and absence of XYL-I and XYL-II. Table 2 describes the substrates employed in these studies. The monosaccharide composition of each substrate was analyzed by HPLC after complete enzymatic hydrolysis to monosaccharides. TABLE 2 Substrates For The Hydrolysis Experiments Xylose Arabinose MeGlcA Xylan Plant Source (% of dw) (% of dw) (% of dw) Unsubstituted xylan Beech Lenzing 100 — <2 AG 4-O-MeGlcA-xylan Birch Roth 86 — 9 Ac-4-O-MeGlcA-xylan* Birch VTT 69 — 5 Arabinoxylan Oat spelts Sigma 67 6 <2 Arabinoxylan** Wheat Megazyme 63 21 nd Arabinoxylan Rye Megazyme 43 25 nd

[0137] XYL-IV was compared to XYL-I and XYL-II in an experiment in which a small amount of each enzyme was employed and only a small proportion (typically <10%) of each substrate was hydrolyzed. Reducing sugars formed by the enzymes were assayed with the DNS method, which is known in the art. Linear xylo-oligosaccharides (1-mers to 5-mers, Xyl₁ to Xyl₅) were determined by HPLC using commercial oligosaccharides as standards. The hydrolysis was studied under conditions of: 24 hr, 40° C., pH 4.0 (XYL I and XYL IV) and pH 5.0 (XYL II). The results of these studies are shown in Table 3. TABLE 3 Hydrolysis of Xylans (5 g/l) By XYLs-I, -II, and -IV of Trichoderma reesei. Reducing Xyl Xyl₂ Xyl₃ Xyl₄ Xyl₅ Total⁺ Substrate Enzyme Sugars (g/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) Unsubstituted xylan XYL I — <4 <4 <4 <4 <4 <4 XYL II 0.12 <4 <4 11 10 11 32 XYL IV 0.44 430 93 <4 <4 <4 523 MeGlcA-xylan XYL I 0.18 <4 7 16 13 16 52 XYL II 0.49 <4 68 110 71 65 314 XYL IV 0.52 370 110 <4 <4 <4 480 Ac-MeGlcA-xylan* XYL I 1.08 63 110 220 190 240 823 XYL II 0.65 7 67 72 75 100 321 XYL IV 1.16 170 1040 200 26 21 1457 Oat spelt arabinoxylan XYL I 0.17 <4 6 13 11 11 41 XYL II 0.81 <4 330 430 145 50 955 XYL IV 0.34 200 26 <4 <4 <4 226 Wheat arabinoxylan XYL I 1.12 24 120 115 31 4 294 XYL II 1.40 18 300 110 9 4 441 XYL IV 0.29 120 17 <4 <4 <4 137

[0138] In these experiments, XYL-IV exhibited greater activity toward unsubstituted xylan and acetylated MeGlcA-xylan, compared to XYLs-I and -II. Both XYL-IV and -II hydrolyzed deacetylated MeGlcA-xylan. XYL-II exhibited greater activity than XYL-IV toward arabinoxylans. XYL-IV produced xylose as its main product, with lesser amounts of xylobiose and substituted xylo-oligosaccharides. The other two xylanases produced a very different product mixture (Table 3). The products and activity of XYL-IV were different from those of family 11 and family 10 glycosyl hydrolases.

[0139] Substrate specificity of XYL-IV was further characterized by employing several isolated oligosaccharide substrates (Table 4). The hydrolysis was studied under conditions of: pH 4.0, 40° C., 1 h. TABLE 4 Hydrolysis of Substituted Oligosaccharides (0.5-0.7 g/l) by XYL-IV of T. reesei (500 nkat/g) Oligosaccharides Products HexA²Xyl₂ + HexA³Xyl₃ HexA²Xyl₂ + Xyl Ara²Xyl₃* No action Ara²Xyl₄ + Ara³Xyl₄* AraXyl₃ + AraXyl₄**

[0140] In these experiments, XYL-IV cleaved the link between two unsubstituted xylose units, but not the link between a substituted and an unsubstituted xylose unit. XYL-IV did, however, cleave closer to the substituted unit than either XYL-I or -II. XYL-UV left only one substituted unit on the reducing end of the oligosaccharide.

[0141] The amount of XYL-UV needed for efficient hydrolysis of HexA³Xyl₃ was evaluated by incubating a mixture of Hex²Xyl₂+Hex³Xyl₃ for 1 h at 40° C. Almost complete hydrolysis of HexA³Xyl₃ was obtained using 30 mg (500 nkat) of XYL-IV per gram of HexA³Xyl₃ (Table 5, FIG. 4). TABLE 5 Hydrolysis of HexA³Xyl₃ by XYL-IV Dosage Dosage HexAXyl₃ HexAXyl₂ Xyl Xyl₂ (mg/g) (nkat/g) (mg/l) (mg/l) (mg/l) (mg/l) 0 0 270 115 <4 7 0.65 10 260 130 6 9 3.2 51 220 160 18 7 6.5 104 150 190 30 8 32 512 13 270 30 8 65 1040 <4 290 66 9 324 5200 <4 290 67 8 648 10400 <4 290 65 8

[0142] XYL-IV was effective for hydrolysis of several polymeric xylans from rye, unsubstituted xylan, MeGlcA-xylan, and arabinoxylan. Arabinoxylan was cleaved more slowly than the other two xylans, which were cleaved at approximately equal rates (FIG. 5).

Example 3 Substrate Hydrolysis by Combinations or Mixtures of XYLs-I, -II, and -IV

[0143] Hydrolysis of several substrates either simultaneously or sequentially with XYLs-I, -II, and -IV demonstrated that XYL-IV exhibits synergy with the other xylanases.

[0144] Table 6 and FIG. 6 show the results of a study in which a substrate was incubated individually with one of XYLs-I, -II, or -IV, or with a combination of these xylanases. The effect of added XYL-IV was more than additive. That is, synergy was observed. Although not limiting to the present invention, it is believed that this synergy is mainly due to XYL-IV's ability to hydrolyze linear and substituted oligosaccharides produced by XYL I and II. TABLE 6 Synergy of XYL-IV With XYLs-I and -II Reducing Dosage sugars Xyl Xyl₂ Xyl₃ Xyl₄ Xyl₅ Tot* Tot_(xyl)** Substrate Enzyme (nkat/g) (g/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) Unsubstituted XYL I 100 0 *** xylan XYL II 100 0 XYL IV 20 0.02 XYL I + IV 100 + 20 0.02 XYL II + 100 + 20 0.03 IV MeGlcA- XYL I 100 0.23 <4 6 13 12 14 45 49 xylan**** XYL II 100 0.14 6 4 11 10 10 41 38 XYL IV 20 0.09 50 9 <4 <4 <4 59 60 XYL I + IV 100 + 20 0.66 420 69 <4 <4 <4 489 493 XYL II + 100 + 20 0.39 260 35 <4 <4 <4 295 297 IV Ac-MeGlcA- XYL I 100 0.86 17 47 100 96 130 390 425 xylan***** XYL II 100 0.11 <4 18 38 53 63 172 188 XYL IV 20 0.58 16 16 5 <4 <4 37 39 XYL I + IV 100 + 20 1.19 270 210 82 81 91 734 772 XYL II + 100 + 20 0.90 190 110 67 47 72 486 512 IV Rye XYL I 100 0.76 4 20 21 14 7 66 71 arabinoxylan XYL II 100 0.81 <4 45 25 10 5 85 92 XYL IV 20 0.03 14 <4 <4 <4 <4 14 14 XYL I + IV 100 + 20 0.98 175 19 <4 <4 <4 194 195 XYL II + 100 + 20 1.14 220 31 5 <4 <4 256 259 IV

[0145] Table 7 and FIG. 7 show the results of a study in which a substrate was incubated with XYL-I, this enzyme was heat inactivated, and then the substrate was incubated with XYL-IV. This resulted sequential cleavage of the substrate by XYL-I followed by XYL-IV. Once again, synergy was observed between XYL-I and XYL-IV. TABLE 7 Stepwise Hydrolysis By XYL-I Followed by XYL-IV XYL I Dosage Xyl Xyl₂ Xyl₃ Xyl₄ Xyl₅ Tot* Tot_(xyl)** Substrate Enzyme (nkat/g) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) (mg/l) MeGlc-xylan XYL I 100 16 195 310 200 120 841 913 XYL I then 100 600 480 <4 <4 <4 1080 1111 XYL IV XYL I 5000 360 1040 240 58 34 1732 1828 XYL I then 5000 750 1160 <4 <4 <4 1910 1984 XYL IV Rye XYL I 100 <4 15 23 12 7 57 62 arabinoxylan XYL I then 100 180 46 <4 <4 <4 226 229 XYL IV XYL I 5000 45 64 <4 <4 <4 109 113 XYL I then 5000 220 76 <4 <4 <4 296 301 XYL IV

Example 4 Preparation of a Cloned DNA Molecule Encoding Trichoderma XYL-IV

[0146] The following is provided as a method of preparing a clone including an entire xyl4 gene described in Example 1. In this example, genomic DNA or cDNA clones derived from Trichoderma are prepared by using the following procedure. A pair of oligonucleotides suitable for use as PCR primers and based on the cDNA sequence of SEQ ID NO: 1 are synthesized. Polymerase chain reaction (PCR) is performed using these primers and, as a template, total genomic DNA isolated from Trichoderma reesei, for example, strain QM6a (ATCC 13631). The DNA polymerase enzyme (e.g., Pwo polymerase), buffer and deoxynucleotide mixture used are supplied by Boehringer Mannheim. Typical conditions are used for PCR, such as; step 1, 1 min. at 94° C.; step 2, 40 sec. at 92° C.; step 3, 1 min. at 50° C., step 4, 2 min. at 72° C.; steps 2, 3 and 4 repeated 29 times; step 5, 5 min. at 72° C.

[0147] The major DNA product of PCR is digested with restriction enzymes, e.g., BglII and XbaI, recognizing sites added by the two primers and the resulting fragment is purified from an agarose electrophoresis gel. This DNA fragment is ligated with an appropriate vector that has been digested with the same restriction enzymes, for example, pSL1180 (Pharmacia) which had been digested with, e.g., BglII and XbaI. The resulting plasmid is typically sequenced to confirm that the insert corresponds to the expected fragment of the Trichoderma xyl4 gene. The DNA sequence reveals the presence of any introns and exons in the gene.

[0148] The plasmid, or the insert it contains, can now be used as a hybridization probe to allow the entire xyl4 gene to be cloned from any genomic DNA or cDNA libraries of interest. Because there are not CBD or linker (hinge) regions, the XYL-IV encoding DNA within the plasmid does not include these regions. Therefore, by design, it would be expected to hybridize with other xyl4 DNA sequences but not to CBD encoding sequences which may be part of other xylanase or glycosidase genes.

[0149] Total genomic DNA from T. reesei, for example, strain QM6a, is digested separately with a variety of different restriction endonucleases and subjected to agarose gel electrophoresis. The DNA was subsequently blotted to a Nytran (S&S) membrane filter and probed with suitable xyl4 DNA fragment isolated from the plasmid and labeled with ³²P by the Megaprime random labeling system supplied by Amersham. Hybridization with the probe was performed at moderate stringency in a typical buffer, for example, containing 30% formamide, 5× SSPE, 0.5% SDS at 38° C. The membrane filter was subsequently washed at moderate stringency, for example, in 2× SSC, 0.1% SDS at 55° C. before being exposed to X-ray film. The results indicate that the genomic copy of the T. reesei xyl4 gene resides on an appropriate restriction fragment.

[0150] Given the exemplified xyl4 gene as provided above, it would be routine for one of skill in the art to clone the Trichoderma reesei xyl4 gene from genomic DNA or cDNA libraries by colony hybridization using a PCR fragment inserted in a plasmid as described above as a probe.

Example 5 Method of Isolating DNA Sequences Encoding XYL-IVs In Microorganisms

[0151] The general technique in Examples 1 and 4 may be adapted in conjunction with known techniques to obtain clones including XYL-IV genes from other fungi and bacteria. A suitable plasmid or an isolated DNA insert encoding part of the xyl4 gene may be labeled as can the whole molecule of the xyl4. This DNA probe can then be used to hybridize with genomic DNA or cDNA from other fungi or bacteria. A comparison of the deduced amino acid sequence of the Trichoderma XYL-IV with the known amino acid sequences of other xylanases identifies certain regions of amino acids that are conserved between XYL-IV and other xylanases. These conserved regions provide the basis for designing degenerate primers for use in PCR amplification of XYL-IV-encoding DNA from other microorganisms. Such methods are generally known in the art and considered routine (see e.g., McPherson, et al., PCR A PRACTICAL APPROACH pp. 171-186 (1991)). The oligonucleotides derived from one or more of these amino acid sequences would be used as primers for routine PCR experiments using genomic DNA. Genomic DNA or cDNA could then easily be obtained from any microorganism and used as a template in such PCR experiments. In this way it would be possible to clone genes encoding a XYL-IV from a variety of microorganisms.

Example 6 Heterologous Hybridization Method for Isolating XYL-IV Encoding Sequences from other Microorganisms

[0152] Genomic DNA from different microorganisms can be digested with an appropriate restriction enzyme, such as HindIII, and run on a 1.0% agarose gel. The gel is depurinated, denatured and blotted, and the membrane is UV-crosslinked by known procedures. Prehybridization, hybridization, labeling of the probe and detection are done using known methods, such as the DIG/Genius™ System from Boehringer Mannheim.

[0153] A probe corresponds to the nucleotide sequence encoding the whole molecule of T. reesei XYL-IV. The original cDNA subclone (EXAMPLE 1) is digested with an appropriate pair of restriction enzymes and the resulting fragment is labeled with DIG-dUTP (digoxigenin-dUTP) via random-primed labeling according to manufacturer's (Boehringer Mannheim) instructions.

[0154] The membrane is prehybridized and then hybridized in an appropriate blocking reagent, such as 5× SSC-0.1% N-lauroylsarcosine-0.02% SDS-1% Genius™ blocking reagent, at a suitable temperature, such as 45° C. Hybridization (typically over night) is followed by washes. Then detection with an appropriate conjugate and visualization, such as with a chemiluminescence substrate CSPD®, are done according to manufacturer's instructions.

[0155] This method and variations of it (different hybridization and washing conditions) can be used to detect XYL-IV encoding genes from any organism.

[0156] The invention has been described with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications may be made while remaining within the spirit and scope of the invention.

1 3 1 1518 DNA Artificial Sequence cDNA clone from Trichoderma reesei RNA 1 cttctctcta ctttctcctc gacatgaagt catctatctc tgttgttttg gctcttctgg 60 gccatagcgc tgcatggtca tacgccacca agtctcaata cagggctaac atcaagatca 120 atgcccgcca gacctatcag acgatgattg gagggggttg ttcgggcgcc tttggtattg 180 cttgtcagca attcgggtct tctggtctgt cgcctgagaa ccaacagaag gttacccaga 240 ttctcttcga tgagaacatt ggcggcctgt ctattgttcg gaatgatatc ggctcctcgc 300 caggaaccac cattttgcca acctgtcccg cgacgccgca agacaagttc gactatgtgt 360 gggatggcag tgacaactgc cagtttaacc tcaccaaaac agctctcaaa tacaatccga 420 acctttacgt ttacgcggat gcctggtccg ctcccggctg catgaagacg gtcgggactg 480 agaacctcgg agggcaaatc tgcggtgtgc gaggaaccga ttgcaaacac gactggcgcc 540 aagcatatgc cgattatctc gtacaatatg tccgcttcta taaagaagaa ggcatcgata 600 tctcccttct aggcgcctgg aacgagccag acttcaaccc ctttacctac gagagcatgc 660 tttccgacgg atatcaagcc aaagactttt tggaggttct ctatcctacg ctcaagaagg 720 ctttcccgaa agtagacgtc agctgctgcg atgcaactgg cgcccgccaa gagagaaaca 780 ttctttatga gctccagcag gcgggtggcg agagatactt tgacattgcg acatggcaca 840 actaccaaag caacccagag cgcccattca acgccggtgg aaagccaaac atacagactg 900 agtgggcaga tggcacgggt ccatggaaca gcacctggga ttatagcggc caacttgctg 960 agggcctcca atgggcatta tatatgcaca acgcgtttgt caacagcgac acctcaggct 1020 acacgcactg gtggtgtgca cagaacacca acggcgacaa cgccctcatc cgccttgatc 1080 gcgacagcta cgaggtgtcg gctcgccttt gggcttttgc ccaatacttc cgctttgccc 1140 ggcccggatc tgtccgcatt ggtgcaacaa gcgacgtcga gaacgtctat gtgaccgcat 1200 atgtcaacaa gaatggaacc gttgctattc ccgtcatcaa cgccgctcac tttccttacg 1260 accttacaat cgatctggag ggtatcaaga agaggaagct gagcgagtac ttgacggaca 1320 atagccacaa cgtcaccttg caaagtcggt acaaggtctc tggtagcagt ctgaaggtga 1380 ctgttgagcc gagagcgatg aagacttttt ggttggagta agaactcgta cgggacgatg 1440 ggaagtgtcg tgaccgtgta tacttttttc acataggccg caatcgacgt ttgccgtcat 1500 atgagcaggg aaaaaaaa 1518 2 465 PRT Trichoderma reesei 2 Met Lys Ser Ser Ile Ser Val Val Leu Ala Leu Leu Gly His Ser Ala 1 5 10 15 Ala Trp Ser Tyr Ala Thr Lys Ser Gln Tyr Arg Ala Asn Ile Lys Ile 20 25 30 Asn Ala Arg Gln Thr Tyr Gln Thr Met Ile Gly Gly Gly Cys Ser Gly 35 40 45 Ala Phe Gly Ile Ala Cys Gln Gln Phe Gly Ser Ser Gly Leu Ser Pro 50 55 60 Glu Asn Gln Gln Lys Val Thr Gln Ile Leu Phe Asp Glu Asn Ile Gly 65 70 75 80 Gly Leu Ser Ile Val Arg Asn Asp Ile Gly Ser Ser Pro Gly Thr Thr 85 90 95 Ile Leu Pro Thr Cys Pro Ala Thr Pro Gln Asp Lys Phe Asp Tyr Val 100 105 110 Trp Asp Gly Ser Asp Asn Cys Gln Phe Asn Leu Thr Lys Thr Ala Leu 115 120 125 Lys Tyr Asn Pro Asn Leu Tyr Val Tyr Ala Asp Ala Trp Ser Ala Pro 130 135 140 Gly Cys Met Lys Thr Val Gly Thr Glu Asn Leu Gly Gly Gln Ile Cys 145 150 155 160 Gly Val Arg Gly Thr Asp Cys Lys His Asp Trp Arg Gln Ala Tyr Ala 165 170 175 Asp Tyr Leu Val Gln Tyr Val Arg Phe Tyr Lys Glu Glu Gly Ile Asp 180 185 190 Ile Ser Leu Leu Gly Ala Trp Asn Glu Pro Asp Phe Asn Pro Phe Thr 195 200 205 Tyr Glu Ser Met Leu Ser Asp Gly Tyr Gln Ala Lys Asp Phe Leu Glu 210 215 220 Val Leu Tyr Pro Thr Leu Lys Lys Ala Phe Pro Lys Val Asp Val Ser 225 230 235 240 Cys Cys Asp Ala Thr Gly Ala Arg Gln Glu Arg Asn Ile Leu Tyr Glu 245 250 255 Leu Gln Gln Ala Gly Gly Glu Arg Tyr Phe Asp Ile Ala Thr Trp His 260 265 270 Asn Tyr Gln Ser Asn Pro Glu Arg Pro Phe Asn Ala Gly Gly Lys Pro 275 280 285 Asn Ile Gln Thr Glu Trp Ala Asp Gly Thr Gly Pro Trp Asn Ser Thr 290 295 300 Trp Asp Tyr Ser Gly Gln Leu Ala Glu Gly Leu Gln Trp Ala Leu Tyr 305 310 315 320 Met His Asn Ala Phe Val Asn Ser Asp Thr Ser Gly Tyr Thr His Trp 325 330 335 Trp Cys Ala Gln Asn Thr Asn Gly Asp Asn Ala Leu Ile Arg Leu Asp 340 345 350 Arg Asp Ser Tyr Glu Val Ser Ala Arg Leu Trp Ala Phe Ala Gln Tyr 355 360 365 Phe Arg Phe Ala Arg Pro Gly Ser Val Arg Ile Gly Ala Thr Ser Asp 370 375 380 Val Glu Asn Val Tyr Val Thr Ala Tyr Val Asn Lys Asn Gly Thr Val 385 390 395 400 Ala Ile Pro Val Ile Asn Ala Ala His Phe Pro Tyr Asp Leu Thr Ile 405 410 415 Asp Leu Glu Gly Ile Lys Lys Arg Lys Leu Ser Glu Tyr Leu Thr Asp 420 425 430 Asn Ser His Asn Val Thr Leu Gln Ser Arg Tyr Lys Val Ser Gly Ser 435 440 445 Ser Leu Lys Val Thr Val Glu Pro Arg Ala Met Lys Thr Phe Trp Leu 450 455 460 Glu 465 3 15 PRT Artificial Sequence an N-terminal amino acid sequence of the mature XYL-IV 3 Xaa Ser Tyr Ala Thr Xaa Ser Gln Tyr Xaa Ala Asn Ile Xaa Ile 1 5 10 15 

We claim:
 1. An isolated nucleic acid comprising DNA having at least 60% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in SEQ ID NO:1, or (b) the complement of the DNA molecule of (a).
 2. The nucleic acid of claim 1, which comprises a DNA molecule encoding the same mature polypeptide encoded by the cDNA in SEQ ID NO:1.
 3. The nucleic acid of claim 1, which comprises a DNA molecule having the nucleotide sequence of SEQ ID NO:1.
 4. The nucleic acid of claim 1, wherein the DNA molecule has at least 70% sequence identity, at least 80% sequence identity, or at least 90% sequence identity.
 5. A nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:1.
 6. A partially or wholly isolated XYL-IV protein derived from a microorganism.
 7. The XYL-IV protein of claim 6, wherein the XYL-IV is derived from a fungus or bacteria.
 8. The XYL-IV protein of claim 7, wherein the fungus comprises a filamentous fungus.
 9. The XYL-IV protein of claim 8, wherein the filamentous fungus comprises Trichoderma spp.; Humicola spp., Neurospora spp., Aspergillus spp., Fusarium spp., Penicillium spp., or Gliocladium spp.
 10. The XYL-IV protein of claim 9, wherein the filamentous fungus comprises Trichoderma reesei.
 11. The XYL-IV protein of claim 6, which comprises (a) an amino acid sequence having at least 70% sequence identity with the amino acid sequence of SEQ ID NO:2 or (b) a derivative of the amino acid sequence of SEQ ID NO:2, wherein the XYL-IV of (a) or (b) cleaves xylan.
 12. The XYL-IV protein of claim 12, wherein the protein has at least 80% sequence identity, at least 90% sequence identity, or at least 95% sequence identity.
 13. The XYL-IV protein of claim 12, which comprises the amino acid sequence of SEQ. ID:NO
 2. 14. An isolated DNA encoding the XYL-IV protein of claim
 6. 15. The DNA of claim 12, wherein the DNA is derived from a fungus or bacteria.
 16. The DNA of claim 15, wherein the fungus comprises a filamentous fungus.
 17. The DNA of claim 16, wherein the filamentous fungus comprises Trichoderma spp., Humicola spp., Neurospora spp., Aspergillus spp., Fusarium spp., Penicillium spp., or Gliocladium spp.
 18. The DNA of claim 17, wherein the filamentous fungus comprises Trichoderma reesei.
 19. The DNA of claim 14, wherein the DNA comprises (a) a nucleotide sequence having at least 85% sequence identity with the nucleotide sequence of SEQ ID NO:1 or (b) a derivative of the nucleotide sequence of SEQ ID NO:1, wherein the DNA of (a) or (b) encodes a XYL-IV protein which cleaves xylan.
 20. An isolated DNA comprising the nucleotide sequence of SEQ ID NO:1.
 21. A vector comprising the DNA of claim
 20. 22. The vector of claim 21 operably linked to control sequences recognized by a host cell transformed with the vector.
 23. A host cell transformed with the vector of claim
 22. 24. The host cell of claim 23, wherein the host cell comprises a filamentous fungus.
 25. The host cell of claim 24, wherein the filamentous fungus comprises Trichoderma spp., Humicola spp., Neurospora spp., Aspergillus spp., or Fusarium spp.
 26. The host cell of claim 25, wherein the filamentous fungus comprises Trichoderma reesei.
 27. A method of producing a XYL-UV protein comprising: (a) obtaining a host cell which has been transformed with a vector comprising DNA encoding a XYL-IV protein; (b) culturing the host cell under conditions suitable for the expression and, optionally, secretion, of the XYL-IV protein; (c) recovering the XYL-IV protein.
 28. The method of claim 27, wherein the DNA is derived from a filamentous fungus.
 29. The method of claim 28, wherein the filamentous fungus comprises Trichoderma spp., Humicola spp., Neurospora spp., Aspergillus spp., Fusarium spp., or Gliocladium spp.
 30. The method of claim 29, wherein the filamentous fungus comprises Trichoderma reesei.
 31. The method of claim 27, wherein the DNA comprises (a) a nucleotide sequence having at least 60% sequence identity with the sequence of SEQ ID NO:1 or (b) a derivative of the nucleotide sequence of SEQ ID NO:1, wherein the DNA encodes a XYL-IV protein which cleaves xylan.
 32. The method of claim 27, wherein the DNA comprises the nucleotide sequence of SEQ ID NO:1.
 33. A method of altering the properties of a xylan containing substrate comprising contacting the xylan containing substrate with a composition comprising XYL-IV protein produced by the method of claim
 27. 34. The method of claim 33, wherein the method comprises altering the handling properties of animal feed and food products and plant materials.
 35. The method of claim 33, wherein the method comprises altering the properties of wood pulp or derivatives thereof during the manufacture of paper.
 36. The method of claim 33, wherein the method comprises altering the properties of xylan containing biomass during its reduction to glucose.
 37. An antibody which specifically binds to a XYL-IV.
 38. The antibody of claim 37, which comprises a monoclonal antibody.
 39. A method of identifying a nucleic acid with homology to a XYL-IV encoding nucleic acid, comprising: hybridizing a test nucleic acid under at least moderately stringent conditions a xyl4 nucleic acid of at least about 14 contiguous nucleotides of DNA having at least 60% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in SEQ ID NO:1, or (b) the complement of the DNA molecule of (a); selecting a test nucleic acid that hybridizes to the xyl4 nucleic acid; isolating the hybridizing test nucleic acid.
 40. The method of claim 39, wherein the hybridizing test nucleic acid encodes a XYL-IV.
 41. The method of claim 39, wherein the hybridizing test nucleic acid encodes a yet uncategorized xylanase.
 42. The method of claim 39, wherein the hybridizing test nucleic acid encodes a xylanase.
 43. The method of claim 39, wherein hybridizing is conducted under highly stringent conditions.
 44. An isolated nucleic acid of at least about 10 nucleotides and comprising DNA having at least 60% sequence identity to (a) a DNA molecule encoding the same mature polypeptide encoded by the cDNA in SEQ ID NO:1, or (b) the complement of the DNA molecule of (a). 